The mechanism by which the assembled polypeptide chain folds to the three-dimensional structure is a subject of intensive studies in many laboratories. We have taken an approach to cracking this second half of the genetic code by investigating a previously unknown non-covalent interaction. Our studies in the previous years have suggested that such new interaction comes to existence in the form of core interaction loop after folding. As described in the previous years we have prepared Type 1, 2, 4 and 5 fragment complexes from horse, tuna, yeast iso-1 or Candida cytochrome c. The different types represent the different sites of the discontinuity of the polypeptide chain. We have shown that the heme and apofragments of Type 1, 2, 4 or 5 complexes are completely exchangeable between any two of the above 4 species. Furthermore, with the exception for two Type H hybrid complexes, all homologous and hybrid Type 1, 2 or 5 complexes exhibit the 695 nm absorbance band. Y. P. Myer and colleagues have shown that the 695 nm bond, indicative of the Met 80-S-heme Fe bond, monitors the integrity of the Trp 59-heme domain. Our results show that the 695 nm band also monitors the structural integrity of the regions above and to the right of heme. Monoclonal 4-128-6 which recognizes the structure above the heme of yeast iso-l -cytochrome c (see the previous reports) was found to cross react with afl Type I and 2 hybrid complexes containing yeast iso- 1 -apofragment or apoprotein. Monoclonal 474-6, recognizing the structure below and to the left of the heme (see the previous reports) was also found to cross react with aH Type 1, but not Type 2, hybrid complexes containing yeast iso- 1apocytochrome c. Combination of two or more mutations occurs in the right channel of the hybrid complexes. The right channel found by R. E. Dickerson and colleagues is formed by close contact of the COOH-terminal helix with the NH2- terminal helix and the heme. Thus, the results suggest that all residues of the right channel are likely exchangeable between any combination of two of eukaryotic cytochrome c species. This, in turn, suggests that the core interaction loop of the right channel is conserved. Thus, the present studies point to the fundamental importance of the core interaction loop in protein folding.